rs1004168

Variant names:

• chr7-48990724-C-A
• rs1004168

Your query was ambiguous. Multiple possible variants found:

• chr7-48990724-C-A
• chr7-48990724-C-G

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 0.321 in 151,972 control chromosomes in the GnomAD database, including 7,972 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 (7972 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0880
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.358 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: 0.321 AC: 48708 AN: 151854 Hom.: 7972 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.321 AC: 48710 AN: 151972 Hom.: 7972 Cov.: 32 AF XY: 0.316 AC XY: 23506 AN XY: 74278

African (AFR) AF: 0.258 AC: 10674 AN: 41444

American (AMR) AF: 0.332 AC: 5067 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1364 AN: 3470

East Asian (EAS) AF: 0.286 AC: 1479 AN: 5164

South Asian (SAS) AF: 0.341 AC: 1643 AN: 4812

European-Finnish (FIN) AF: 0.259 AC: 2734 AN: 10550

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.361 AC: 24567 AN: 67968

Other (OTH) AF: 0.348 AC: 734 AN: 2112

Alfa AF: 0.351 Hom.: 4942

Bravo AF: 0.324

Asia WGS AF: 0.300 AC: 1041 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.59
PhyloP100		0.088

Splicing

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

Other links and lift over

dbSNP: rs1004168; hg19: chr7-49030320;