6-62247340-G-T

Variant names:

• chr6-62247340-G-T
• rs176605
• NM_152688.4:c.91+38518C>A

Variant summary

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

The NM_152688.4(KHDRBS2):​c.91+38518C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 1 in 151,810 control chromosomes in the GnomAD database, including 75,904 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 1.0 (75904 hom., cov: 27)
• Consequence: KHDRBS2 NM_152688.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700
• 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=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.994 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.91+38518C>A		intron	N/A	NP_689901.2	Q5VWX1
	KHDRBS2	NM_001350622.2		c.91+38518C>A		intron	N/A	NP_001337551.1
	KHDRBS2	NR_146870.2		n.368+38518C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KHDRBS2	ENST00000281156.5	TSL:1 MANE Select	c.91+38518C>A		intron	N/A	ENSP00000281156.3	Q5VWX1
	KHDRBS2	ENST00000968831.1		c.91+38518C>A		intron	N/A	ENSP00000638890.1
	KHDRBS2	ENST00000931671.1		c.91+38518C>A		intron	N/A	ENSP00000601730.1

Frequencies

GnomAD3 genomes AF: 1.00 AC: 151691 AN: 151692 Hom.: 75845 Cov.: 27

Gnomad AFR AF: 1.00

Gnomad AMI AF: 1.00

Gnomad AMR AF: 1.00

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 1.00

Gnomad MID AF: 1.00

Gnomad NFE AF: 1.00

Gnomad OTH AF: 1.00

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

GnomAD4 genome AF: 1.00 AC: 151809 AN: 151810 Hom.: 75904 Cov.: 27 AF XY: 1.00 AC XY: 74197 AN XY: 74198

African (AFR) AF: 1.00 AC: 41456 AN: 41456

American (AMR) AF: 1.00 AC: 15238 AN: 15238

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3468 AN: 3468

East Asian (EAS) AF: 1.00 AC: 5074 AN: 5074

South Asian (SAS) AF: 1.00 AC: 4790 AN: 4790

European-Finnish (FIN) AF: 1.00 AC: 10582 AN: 10582

Middle Eastern (MID) AF: 1.00 AC: 294 AN: 294

European-Non Finnish (NFE) AF: 1.00 AC: 67891 AN: 67892

Other (OTH) AF: 1.00 AC: 2104 AN: 2104

Alfa AF: 1.00 Hom.: 8166

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.63
DANN	Benign	0.21
PhyloP100		0.0070
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: rs176605; hg19: chr6-62957245;