rs7549114

Variant names:

• chr1-206629756-G-A
• rs7549114

Variant summary

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

The variant allele was found at a frequency of 0.126 in 152,138 control chromosomes in the GnomAD database, including 1,365 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 0.13 (1365 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19222 AN: 152020 Hom.: 1365 Cov.: 32

Gnomad AFR AF: 0.0925

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0750

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.126 AC: 19222 AN: 152138 Hom.: 1365 Cov.: 32 AF XY: 0.123 AC XY: 9182 AN XY: 74360

African (AFR) AF: 0.0923 AC: 3833 AN: 41522

American (AMR) AF: 0.107 AC: 1632 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.197 AC: 683 AN: 3472

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5190

South Asian (SAS) AF: 0.0755 AC: 364 AN: 4820

European-Finnish (FIN) AF: 0.178 AC: 1878 AN: 10558

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.151 AC: 10271 AN: 67986

Other (OTH) AF: 0.143 AC: 303 AN: 2112

Alfa AF: 0.142 Hom.: 4955

Bravo AF: 0.122

Asia WGS AF: 0.0340 AC: 118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	12
DANN	Benign	0.88
PhyloP100		-0.049

Splicing

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

Other links and lift over

dbSNP: rs7549114; hg19: chr1-206803101;