rs10484619

Variant names:

• chr6-62149908-G-A
• rs10484619
• NM_152688.4:c.219+27277C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-62149908-G-A
• chr6-62149908-G-C
• chr6-62149908-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152688.4(KHDRBS2):​c.219+27277C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0798 in 152,178 control chromosomes in the GnomAD database, including 521 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.080 (521 hom., cov: 33)
• Consequence: KHDRBS2 NM_152688.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 0 publications found

Genes affected

KHDRBS2 (HGNC:18114): (KH RNA binding domain containing, signal transduction associated 2) Predicted to enable mRNA binding activity and poly(A) binding activity. Predicted to be involved in regulation of alternative mRNA splicing, via spliceosome. Predicted to be located in nucleoplasm. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152688.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KHDRBS2	NM_152688.4	MANE Select	c.219+27277C>T		intron	N/A	NP_689901.2	Q5VWX1
	KHDRBS2	NM_001350622.2		c.219+27277C>T		intron	N/A	NP_001337551.1
	KHDRBS2	NR_146870.2		n.496+27277C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KHDRBS2	ENST00000281156.5	TSL:1 MANE Select	c.219+27277C>T		intron	N/A	ENSP00000281156.3	Q5VWX1
	KHDRBS2	ENST00000968831.1		c.219+27277C>T		intron	N/A	ENSP00000638890.1
	KHDRBS2	ENST00000931671.1		c.219+27277C>T		intron	N/A	ENSP00000601730.1

Frequencies

GnomAD3 genomes AF: 0.0799 AC: 12144 AN: 152060 Hom.: 521 Cov.: 33

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0628

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.0385

Gnomad SAS AF: 0.0469

Gnomad FIN AF: 0.0818

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0707

Gnomad OTH AF: 0.0789

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0798 AC: 12137 AN: 152178 Hom.: 521 Cov.: 33 AF XY: 0.0793 AC XY: 5901 AN XY: 74396

African (AFR) AF: 0.104 AC: 4319 AN: 41518

American (AMR) AF: 0.0626 AC: 957 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 560 AN: 3470

East Asian (EAS) AF: 0.0386 AC: 200 AN: 5188

South Asian (SAS) AF: 0.0469 AC: 226 AN: 4816

European-Finnish (FIN) AF: 0.0818 AC: 866 AN: 10582

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0707 AC: 4806 AN: 68000

Other (OTH) AF: 0.0781 AC: 165 AN: 2114

Alfa AF: 0.0763 Hom.: 717

Bravo AF: 0.0798

Asia WGS AF: 0.0510 AC: 175 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.88
DANN	Benign	0.54
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10484619; hg19: chr6-62859813;