chr19-44905371-T-C

Variant names:

• chr19-44905371-T-C
• rs769446

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 0.0708 in 149,116 control chromosomes in the GnomAD database, including 452 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 0.071 (452 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 74 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 = 0.097 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: 0.0709 AC: 10561 AN: 148988 Hom.: 451 Cov.: 32

Gnomad AFR AF: 0.0360

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.0537

Gnomad ASJ AF: 0.0722

Gnomad EAS AF: 0.0932

Gnomad SAS AF: 0.0624

Gnomad FIN AF: 0.0402

Gnomad MID AF: 0.0662

Gnomad NFE AF: 0.0990

Gnomad OTH AF: 0.0771

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

GnomAD4 genome AF: 0.0708 AC: 10558 AN: 149116 Hom.: 452 Cov.: 32 AF XY: 0.0685 AC XY: 4988 AN XY: 72868

African (AFR) AF: 0.0359 AC: 1451 AN: 40394

American (AMR) AF: 0.0537 AC: 802 AN: 14946

Ashkenazi Jewish (ASJ) AF: 0.0722 AC: 249 AN: 3450

East Asian (EAS) AF: 0.0930 AC: 451 AN: 4848

South Asian (SAS) AF: 0.0621 AC: 292 AN: 4704

European-Finnish (FIN) AF: 0.0402 AC: 416 AN: 10346

Middle Eastern (MID) AF: 0.0534 AC: 14 AN: 262

European-Non Finnish (NFE) AF: 0.0990 AC: 6654 AN: 67200

Other (OTH) AF: 0.0788 AC: 163 AN: 2068

Alfa AF: 0.0881 Hom.: 128

Bravo AF: 0.0686

Asia WGS AF: 0.0960 AC: 334 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.48
PhyloP100		-1.4
PromoterAI		0.028	Neutral

Splicing

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

Other links and lift over

dbSNP: rs769446; hg19: chr19-45408628;