rs61779296

Variant names:

• chr1-58577785-G-A
• rs61779296
• ENST00000637377.2:n.161+1409G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-58577785-G-A
• chr1-58577785-G-T

Variant summary

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

The ENST00000767021.1(ENSG00000283445):​n.188+1409G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 164,270 control chromosomes in the GnomAD database, including 7,283 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 0.29 (7095 hom., cov: 33)
  • Exomes 𝑓: 0.17 (188 hom.)
• Consequence: ENSG00000283445 ENST00000767021.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.825
• Publications: 8 publications found

Genes affected

ENSG00000283445 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000767021.1. 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
	ENSG00000283445	ENST00000637377.2	TSL:5	n.161+1409G>A		intron	N/A
	ENSG00000283445	ENST00000767021.1		n.188+1409G>A		intron	N/A
	ENSG00000283445	ENST00000767022.1		n.142+1409G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44427 AN: 151884 Hom.: 7071 Cov.: 33

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.0552

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.297

GnomAD4 exome AF: 0.171 AC: 2098 AN: 12266 Hom.: 188 Cov.: 0 AF XY: 0.173 AC XY: 1023 AN XY: 5904

African (AFR) AF: 0.250 AC: 1 AN: 4

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.00 AC: 0 AN: 4

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.170 AC: 2055 AN: 12082

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.191 AC: 18 AN: 94

Other (OTH) AF: 0.303 AC: 23 AN: 76

GnomAD4 genome AF: 0.293 AC: 44487 AN: 152004 Hom.: 7095 Cov.: 33 AF XY: 0.282 AC XY: 20975 AN XY: 74340

African (AFR) AF: 0.419 AC: 17341 AN: 41376

American (AMR) AF: 0.228 AC: 3493 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 955 AN: 3466

East Asian (EAS) AF: 0.0552 AC: 286 AN: 5184

South Asian (SAS) AF: 0.201 AC: 968 AN: 4826

European-Finnish (FIN) AF: 0.171 AC: 1816 AN: 10592

Middle Eastern (MID) AF: 0.401 AC: 117 AN: 292

European-Non Finnish (NFE) AF: 0.272 AC: 18491 AN: 67954

Other (OTH) AF: 0.294 AC: 620 AN: 2112

Alfa AF: 0.277 Hom.: 1218

Bravo AF: 0.302

Asia WGS AF: 0.147 AC: 513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.87
DANN	Benign	0.53
PhyloP100		-0.82

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: rs61779296;

hg19: chr1-59043457;

COSMIC: COSV64666973;