rs7601770

Variant names:

• chr2-62431121-T-C
• rs7601770
• ENST00000416845.2:n.152+15692T>C

Variant summary

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

The ENST00000416845.2(ENSG00000228541):​n.152+15692T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 151,840 control chromosomes in the GnomAD database, including 8,489 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 0.32 (8489 hom., cov: 30)
• Consequence: ENSG00000228541 ENST00000416845.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.42
• Publications: 2 publications found

Genes affected

ENSG00000228541 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000416845.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000228541	ENST00000416845.2	TSL:3	n.152+15692T>C		intron	N/A
	ENSG00000228541	ENST00000689590.2		n.199-32718T>C		intron	N/A
	ENSG00000228541	ENST00000807679.1		n.303-10613T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49207 AN: 151722 Hom.: 8492 Cov.: 30

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.0294

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.324 AC: 49219 AN: 151840 Hom.: 8489 Cov.: 30 AF XY: 0.314 AC XY: 23285 AN XY: 74194

African (AFR) AF: 0.320 AC: 13253 AN: 41370

American (AMR) AF: 0.251 AC: 3828 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1071 AN: 3466

East Asian (EAS) AF: 0.0289 AC: 150 AN: 5186

South Asian (SAS) AF: 0.195 AC: 937 AN: 4810

European-Finnish (FIN) AF: 0.328 AC: 3447 AN: 10512

Middle Eastern (MID) AF: 0.291 AC: 85 AN: 292

European-Non Finnish (NFE) AF: 0.375 AC: 25508 AN: 67932

Other (OTH) AF: 0.308 AC: 649 AN: 2108

Alfa AF: 0.342 Hom.: 1464

Bravo AF: 0.315

Asia WGS AF: 0.109 AC: 381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.16
DANN	Benign	0.53
PhyloP100		-2.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7601770;

hg19: chr2-62658256;