NM_152688.4:c.811-47214T>C

Variant names:

• chr6-61779978-A-G
• rs1201494
• NM_152688.4:c.811-47214T>C

Variant summary

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

The NM_152688.4(KHDRBS2):​c.811-47214T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.657 in 151,902 control chromosomes in the GnomAD database, including 33,532 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 0.66 (33532 hom., cov: 31)
• Consequence: KHDRBS2 NM_152688.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.679
• 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KHDRBS2	NM_152688.4	c.811-47214T>C		intron_variant	Intron 6 of 8	ENST00000281156.5	NP_689901.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KHDRBS2	ENST00000281156.5	c.811-47214T>C		intron_variant	Intron 6 of 8	1	NM_152688.4	ENSP00000281156.3
KHDRBS2	ENST00000675091.1	n.811-47214T>C		intron_variant	Intron 6 of 9			ENSP00000502245.1
KHDRBS2	ENST00000718012.1	n.811-47214T>C		intron_variant	Intron 6 of 13			ENSP00000520654.1

Frequencies

GnomAD3 genomes AF: 0.657 AC: 99666 AN: 151784 Hom.: 33479 Cov.: 31

Gnomad AFR AF: 0.807

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.703

Gnomad FIN AF: 0.634

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.619

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

GnomAD4 genome AF: 0.657 AC: 99774 AN: 151902 Hom.: 33532 Cov.: 31 AF XY: 0.658 AC XY: 48846 AN XY: 74222

African (AFR) AF: 0.807 AC: 33471 AN: 41468

American (AMR) AF: 0.597 AC: 9108 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.670 AC: 2323 AN: 3468

East Asian (EAS) AF: 0.524 AC: 2696 AN: 5142

South Asian (SAS) AF: 0.703 AC: 3383 AN: 4814

European-Finnish (FIN) AF: 0.634 AC: 6650 AN: 10492

Middle Eastern (MID) AF: 0.603 AC: 176 AN: 292

European-Non Finnish (NFE) AF: 0.592 AC: 40210 AN: 67946

Other (OTH) AF: 0.621 AC: 1313 AN: 2114

Alfa AF: 0.628 Hom.: 3932

Bravo AF: 0.658

Asia WGS AF: 0.677 AC: 2353 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.83
DANN	Benign	0.35
PhyloP100		-0.68
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: rs1201494; hg19: chr6-62489883;