rs1357978

Variant names:

• chr7-13520596-C-A
• rs1357978
• ENST00000411542.1:n.352-116050C>A

Your query was ambiguous. Multiple possible variants found:

• chr7-13520596-C-A
• chr7-13520596-C-G
• chr7-13520596-C-T

Variant summary

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

The ENST00000411542.1(ENSG00000229618):​n.352-116050C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 152,082 control chromosomes in the GnomAD database, including 4,063 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 0.21 (4063 hom., cov: 32)
• Consequence: ENSG00000229618 ENST00000411542.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.275
• Publications: 7 publications found

Genes affected

ENSG00000229618 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986770	XR_001745097.2	n.148-181720C>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000229618	ENST00000411542.1	n.352-116050C>A		intron_variant	Intron 3 of 4	4
ENSG00000229618	ENST00000638964.1	n.724-116050C>A		intron_variant	Intron 3 of 5	5
ENSG00000229618	ENST00000639998.1	n.723-116050C>A		intron_variant	Intron 5 of 7	5

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31285 AN: 151964 Hom.: 4061 Cov.: 32

Gnomad AFR AF: 0.0794

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.00251

Gnomad SAS AF: 0.0825

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.206 AC: 31281 AN: 152082 Hom.: 4063 Cov.: 32 AF XY: 0.202 AC XY: 15020 AN XY: 74310

African (AFR) AF: 0.0793 AC: 3292 AN: 41520

American (AMR) AF: 0.203 AC: 3106 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 859 AN: 3468

East Asian (EAS) AF: 0.00252 AC: 13 AN: 5166

South Asian (SAS) AF: 0.0826 AC: 398 AN: 4820

European-Finnish (FIN) AF: 0.299 AC: 3148 AN: 10544

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.289 AC: 19647 AN: 67966

Other (OTH) AF: 0.220 AC: 465 AN: 2112

Alfa AF: 0.231 Hom.: 607

Bravo AF: 0.195

Asia WGS AF: 0.0490 AC: 169 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.18
DANN	Benign	0.25
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs1357978; hg19: chr7-13560221;