19-44905307-A-T

Variant names:

• chr19-44905307-A-T
• rs449647

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 0.209 in 150,672 control chromosomes in the GnomAD database, including 3,648 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 0.21 (3648 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.552
• Publications: 141 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.293 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: 0.208 AC: 31386 AN: 150554 Hom.: 3639 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.100

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.0302

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.209 AC: 31417 AN: 150672 Hom.: 3648 Cov.: 32 AF XY: 0.206 AC XY: 15146 AN XY: 73602

African (AFR) AF: 0.298 AC: 12191 AN: 40968

American (AMR) AF: 0.224 AC: 3383 AN: 15108

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 962 AN: 3458

East Asian (EAS) AF: 0.0303 AC: 154 AN: 5090

South Asian (SAS) AF: 0.209 AC: 994 AN: 4766

European-Finnish (FIN) AF: 0.121 AC: 1248 AN: 10300

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.174 AC: 11797 AN: 67690

Other (OTH) AF: 0.234 AC: 490 AN: 2098

Alfa AF: 0.202 Hom.: 386

Bravo AF: 0.216

Asia WGS AF: 0.128 AC: 443 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.0
DANN	Benign	0.81
PhyloP100		0.55
PromoterAI		0.035	Neutral

Splicing

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

Other links and lift over

dbSNP: rs449647; hg19: chr19-45408564;