chr6-121061772-T-C

Variant names:

• chr6-121061772-T-C
• rs443076

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 0.225 in 136,228 control chromosomes in the GnomAD database, including 4,090 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 0.22 (4090 hom., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.407
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.403 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: 0.225 AC: 30577 AN: 136184 Hom.: 4087 Cov.: 23

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.225 AC: 30598 AN: 136228 Hom.: 4090 Cov.: 23 AF XY: 0.224 AC XY: 14758 AN XY: 65862

African (AFR) AF: 0.409 AC: 13984 AN: 34190

American (AMR) AF: 0.303 AC: 4085 AN: 13496

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 471 AN: 3338

East Asian (EAS) AF: 0.189 AC: 882 AN: 4676

South Asian (SAS) AF: 0.172 AC: 770 AN: 4470

European-Finnish (FIN) AF: 0.103 AC: 807 AN: 7860

Middle Eastern (MID) AF: 0.164 AC: 44 AN: 268

European-Non Finnish (NFE) AF: 0.139 AC: 9039 AN: 65190

Other (OTH) AF: 0.221 AC: 409 AN: 1852

Alfa AF: 0.170 Hom.: 180

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.87
DANN	Benign	0.57
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs443076; hg19: chr6-121382918;