NM_001195243.2:c.4-4603T>G

Variant names:

• chr7-129507644-T-G
• rs11771549
• NM_001195243.2:c.4-4603T>G

Variant summary

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

The NM_001195243.2(SMKR1):​c.4-4603T>G 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 152,066 control chromosomes in the GnomAD database, including 33,350 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 (33350 hom., cov: 33)
• Consequence: SMKR1 NM_001195243.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360
• Publications: 6 publications found

Genes affected

SMKR1 (HGNC:43561): (small lysine rich protein 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SMKR1	NM_001195243.2	c.4-4603T>G		intron_variant	Intron 1 of 1	ENST00000462322.3	NP_001182172.1
SMKR1	XM_024446620.2	c.65-4607T>G		intron_variant	Intron 1 of 1		XP_024302388.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMKR1	ENST00000462322.3	c.4-4603T>G		intron_variant	Intron 1 of 1	1	NM_001195243.2	ENSP00000454370.1
SMKR1	ENST00000488846.1	n.37-4607T>G		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.656 AC: 99747 AN: 151948 Hom.: 33319 Cov.: 33

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.943

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.659

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

GnomAD4 genome AF: 0.657 AC: 99837 AN: 152066 Hom.: 33350 Cov.: 33 AF XY: 0.663 AC XY: 49278 AN XY: 74342

African (AFR) AF: 0.545 AC: 22583 AN: 41458

American (AMR) AF: 0.675 AC: 10312 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.650 AC: 2256 AN: 3470

East Asian (EAS) AF: 0.942 AC: 4889 AN: 5188

South Asian (SAS) AF: 0.714 AC: 3445 AN: 4822

European-Finnish (FIN) AF: 0.733 AC: 7754 AN: 10574

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.685 AC: 46576 AN: 67966

Other (OTH) AF: 0.663 AC: 1399 AN: 2110

Alfa AF: 0.672 Hom.: 58858

Bravo AF: 0.646

Asia WGS AF: 0.838 AC: 2914 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.51
PhyloP100		-0.036
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: rs11771549; hg19: chr7-129147485;