rs1204116

Variant names:

• chr6-61694191-C-A
• rs1204116
• NM_152688.4:c.952+3004G>T

Your query was ambiguous. Multiple possible variants found:

• chr6-61694191-C-A
• chr6-61694191-C-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.952+3004G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,080 control chromosomes in the GnomAD database, including 3,546 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 0.20 (3546 hom., cov: 33)
• Consequence: KHDRBS2 NM_152688.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.534
• Publications: 2 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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.32 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.952+3004G>T		intron	N/A	NP_689901.2	Q5VWX1
	KHDRBS2	NM_001350622.2		c.1003+3004G>T		intron	N/A	NP_001337551.1
	KHDRBS2	NR_146870.2		n.1229+3004G>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.952+3004G>T		intron	N/A	ENSP00000281156.3	Q5VWX1
	KHDRBS2	ENST00000968831.1		c.952+3004G>T		intron	N/A	ENSP00000638890.1
	KHDRBS2	ENST00000931671.1		c.805+3004G>T		intron	N/A	ENSP00000601730.1

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30102 AN: 151962 Hom.: 3541 Cov.: 33

Gnomad AFR AF: 0.0840

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.198 AC: 30116 AN: 152080 Hom.: 3546 Cov.: 33 AF XY: 0.206 AC XY: 15296 AN XY: 74312

African (AFR) AF: 0.0841 AC: 3492 AN: 41528

American (AMR) AF: 0.199 AC: 3042 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 762 AN: 3468

East Asian (EAS) AF: 0.169 AC: 874 AN: 5160

South Asian (SAS) AF: 0.333 AC: 1606 AN: 4818

European-Finnish (FIN) AF: 0.353 AC: 3728 AN: 10546

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.234 AC: 15918 AN: 67978

Other (OTH) AF: 0.193 AC: 407 AN: 2114

Alfa AF: 0.213 Hom.: 1958

Bravo AF: 0.178

Asia WGS AF: 0.255 AC: 888 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.056
DANN	Benign	0.24
PhyloP100		-0.53
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: rs1204116; hg19: chr6-62404096;